Computing the Role of Near Attack Conformations in an Enzyme-Catalyzed Nucleophilic Bimolecular Reaction

Abstract

Near attack conformations (NACs) are conformations extending from the ground state (GS) that lie on the transition path of a chemical reaction. Here, we develop a method for computing the thermodynamic contribution to catalysis due to NAC formation in bimolecular reactions, within the limit of a classical molecular dynamics force field. We make use of the Bürgi–Dunitz theory applied to large-scale unbiased all-atom ensemble molecular dynamics simulations. We apply this to HIV-1 protease peptide hydrolysis, known to achieve a rate enhancement of ∼1011 (ΔGcat⧧ ∼ 15 kcal/mol) over the uncatalyzed bimolecular reaction (ΔGnon⧧ ∼ 30 kcal/mol). The ground state consists of a nucleophilic water molecule bound to an octapeptide substrate in the active site. We first observe multiple and reversible binding of a nucleophilic water molecule into the active site giving a free energy of binding of ΔG = −1 kcal/mol to form the GS. The free energy barriers for catalyzed and uncatalyzed NAC formation are both equivalent: ΔGNAC⧧ = 4.6 kcal/mol, constituting ∼30% and ∼15% of the overall barriers, respectively. Therefore, not only does adoption of NACs only account for minor progress along the transition path in both catalyzed and uncatalyzed reactions, but there is no preferential formation of them in the catalyzed reaction. Analysis of the catalytic hydrogen bond network reveals interactions that stabilize the GS; however, subsequent NAC formation does not preferentially favor any of the possible hydrogen bond configurations. This supports the view that the catalytic power of HIV-1 protease is not due to NAC formation.

Conformational flexibility of PPII-helix: A density functional theory study

“…Thus, the unoccupied * orbits of carbonyl group expose to the electron cloud of donor oxygen by different orientations and are presented by the n-* interactions. It is just like a nucleophilic attack of carbonyls that nucleophiles approach the carbonyl plane at a Bürgi-Dunitz angle about 105 ± 5 • rather than perpendicular to the carbonyl system [42,43]. From this view, the geometrical parameters of carbonyl pyramidalization become a method to decide the strength of n-* interactions.…”

Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease

“…mol -1 . 46 This contribution was added to all barriers. We ran another 5 ns MD with this new Hamiltonian.…”

Reactivation of VX-Inhibited Human Acetylcholinesterase by Deprotonated Pralidoxime. A Complementary Quantum Mechanical Study

“…In our recent work, we presented molecular modeling studies meant to contribute to a better understanding of the reactivation mechanism of HssAChE inhibited by the nerve agent O-ethyl S-(2-(diisopropylamino)ethyl) methylphosphonothioate (VX) [20]. In that case, classical molecular-dynamics (MD) simulations were performed, considering the near attack conformation (NAC) approach [20][21][22], on a model of HssAChE based on the experimental structure of mouse AChE (PDB code 3ZLV). As a result, a NAC frame of deprotonated-2-PAM in the CAS of VX-inhibited HssAChE was obtained [20].…”

“…As a result, a NAC frame of deprotonated-2-PAM in the CAS of VX-inhibited HssAChE was obtained [20]. The deprotonation of the aldoxime (−C=NOH) group may happen under physiologic conditions in the pathway towards the NAC [14,19,[21][22][23], or before its entry into the AChE active site, according to the pKa = 7.68 of 2-PAM [24]. In our NAC, the distance between the O-atom of the aldoximate (−C=NO − ) group and the P-atom of the phosphorylated Ser203 (d OP ) was 3.26 Å and the attack angle amongst the O-and P-atoms of the OP and the O-atom of Ser203 (θ OPO ) was 175 • [20].…”